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Systematic Identification of Optimal HIV-1 CTL Epitopes

Christian Brander1 and Bruce D. Walker2

1AIDS Research Center, Massachusetts General Hospital, 149 13th Street, Room 5234,
2Charlestown, MA 02129, USA, and Harvard Medical School Boston, MA USA

Updated October 1997

Characterization of the cellular immune response against HIV has led to the identification of numerous HLA class I restricted CTL epitopes and many laboratories have contributed to the description of CTL epitopes in most of the HIV-1 proteins. Since the last update of this CTL epitope list in 1996, a number of new epitopes have been published and are included in the current update. References have also been updated for epitopes previously listed as personal communications which have since been published.

For this update, we maintained the same rigid criteria for inclusion in the list of optimal epitopes as in previous years. First, the peptide has to be involved in the natural immune response against HIV. Thus, only epitopes that have been shown to induce a specific CTL response upon HIV infection in vivo are included. Second, the peptides have to be truncated to the size of the optimal epitope, which is the shortest epitope that is recognized at the lowest peptide concentration; and third, the HLA class I restricting molecule has to be identified. We therefore excluded epitopes from the list of optimal epitopes if only the binding to a certain class I molecule has been shown but not the immunogenicity in vivo, or if no peptide titration assay with truncated peptides has been reported. However, those epitopes are included in the extended CTL epitope list in Part-I of this database. Nine newly listed optimal epitopes are included this year, bringing the total number to 110. These epitopes add to the previously identified pattern of CTL epitopes being widely distributed over the expressed HIV proteins.

In order to keep this list updated it would be very helpful for us to receive information about newly identified epitopes as they become available. For comments and/or contributions to this CTL epitope list (C.B. or B.W.) or the main database (B.K.) please call, write, or mail us at:

Bette Korber		Christian Brander		Bruce D. Walker
phone:  505 665 4453    phone:  617 724 5789		phone:  617 724 8332
FAX:    505 665 3493    FAX:    617 726 5411		FAX:    617 726 4691	Brander@Helix.MGH.Harvard.Edu	BWalker@Helix.MGH.Harvard.Edu

Table-1 Best Defined HIV CTL Epitopes

HLA	Protein		AA	Isolate	 	Sequence 	Reference

HLA-A2						2      C	  Falk91
						L      V
						I      L
	p17	      77-85	  LAI		SLYNTVATL       Johnson91,Parker92,Parker94
	RT	     346-354	  LAI		VIYQYMDDL	Harrer96
	RT	     476-484	  LAI		ILKEPVHGV	Walker89,Tsomides91
A*0201	gp120	     311-320	  IIIB		RGPGRAFVTI	Alexander-Miller96
	gp41	     818-827	  LAI		SLLNATDIAV	Dupuis95
	nef	     136-145	  LAI		PLTFGWCYKL	Haas96, B. Maier and B. Autran Per.comm.
	nef	     180-189	  LAI		VLEWRFDSRL	Haas96, B. Maier and B. Autran Per.comm.
	nef	     190-198	  LAI		AFHHVAREL	Hadida95, B. Autran Per.comm.

HLA-A3.1					23     C	DiBrino93
						IF     K
						L      Y	
	p17	      18-26 	  LAI		KIRLRPGGK	Harrer96b
        p17           20-28       LAI           RLRPGGKKK       B. Culmann, D. Lewinsohn, D. Ruhl, S. 
                                                                Riddell, B. Wilkes, Per.comm.,Goulder97
        p17           20-29       LAI           RLRPGGKKKY      B. Wilkes, D. Ruhl Per.comm.
        RT           325-333      LAI           AIFQSSMTK       Threlkeld97
        gp120         37-46       LAI           TVYYGVPVWK      Johnson94
        gp41         775-785      LAI           RLRDLLLIVTR     Takahashi91
        nef           73-82       LAI           QVPLRPMTYK      Koenig90,Culmann91

HLA-A11                                         2      C        Zhang93
                                                I      K
  	p17	      84-92       LAI		TLYCVHQRI	T. Harrer Per.comm.
        p24          349-359      III-B		ACQGVGGPGGHK	Sipsas97
 	RT	     325-333	  LAI		AIFQSSMTK	Johnson94b,Zhang93,Threlkeld97
        RT           508-517	  LAI		IYQEPFKNLK  	B. Culmann Per.comm.
  	nef	      73-82	  LAI		PLRPMTYK	Culmann91
	nef 	      84-92	  LAI		AVDLSHFLK	Culmann91

A*7401 	RT	      71-79       Clade A/B/D	ITLWQRPLV	S. Rowland-Jones Per.comm.

        p17           28-36       LAI		KYKLKHIVW	D. Lewinsohn Per.comm.
	gp120	      53-62	  LAI		LFCASDAKAY	Lieberman92,Shankar96
	gp41	     591-598	  LAI		YLKDQQLL	Dai92
	p24	     145-155	  LAI		QAISPRTLNAW 	I. Kurane, K. West Per.comm.
	p24	     203-212	  LAI		ETINEEAAEW	Klenerman96,vanBaalen96

	p24	     167-175	  LAI	 	EVIPMFSAL	Goulder96b
	RT	     593-603	  LAI		ETFYVDGAANR	B. Wilkes, D. Ruhl Per.comm.

A*6802	RT	      71-79	  Clade A/B/D	ITLWQRPLV	S. Rowland-Jones Per.comm.
A*6802	RT	      85-93	  Clade D	DTVLEEMNL	S. Rowland-Jones Per.comm.

	gp120	     376-384	  LAI		FNCGGEFFY	Wilson97

	gp41	     775-785	  LAI		RLRDLLLIVTR	Safrit94a,Safrit94b

	RT	     559-568	  LAI		PIQKETWETW	Harrer96b
	gp120	     419-427	  HXB2		RIKQIINMW	Harrer96b

HLA-B7						123      C	Englehard93
						APR      L
	p24	     148-156	  LAI		SPRTLNAWV	D. Lewinsohn Per.comm.
	p24	     179-187	  LAI		ATPQDLNTM	B. Wilkes, D. Ruhl Per.comm.
	RT	     323-332	  LAI		SPAIFQSSMT	C. Hey and D. Ruhl, Per.comm.
	gp120	     303-312	  LAI		RPNNNTRKSI	Safrit94b
	gp41	     843-851	  LAI		IPRRIRQGL	B. Wilkes and D. Ruhl, Per.comm.
	nef	      68-77	  LAI		FPVTPQVPLR	Haas96, B. Maier and B. Autran Per.comm.
	nef	      77-85	  LAI		RPMTYKAAL	Bauer97
	nef	     128-137	  LAI		TPGPGVRYPL	CulmannPenciolelli94,Haas96, B. Maier and B. Autran                                                          Per.comm.
HLA-B8						  23 5  C	Hill92b,Sutton93
                                                  P  R  L
						  LK K  I
	p17	      24-31	  LAI		GGKKKYKL	RowlandJones93a,Goulder97
	p17	      74-82	  LAI		ELRSLYNTV	Goulder97c
	p24	     259-267	  LAI		EIYKRWII	Sutton93,Goulder97c	
	gp120	       2-10	  III-B		RVKEKYQHL	Sipsas97
	gp41	     591-598	  LAI		YLKDQQLL	Johnson92,Shankar96
	nef	      13-20	  LAI		WPTVRERM	Goulder97c
	nef	      90-97	  LAI		FLKEKGGL	CulmannPenciolelli94,Price97	

HLA-B14						 23 56  C	DiBrino94b
						 RL RI  L
						    KY HL
	p24	     183-191	  LAI		DLNTMLNTV	Nixon88b,Johnson92
	p24	     298-306	  LAI		DRFYKTLRA	Harrer96b	
	gp41	     589-597	  LAI		ERYLKDQQL	Johnson92	

	gp120	     375-383	  LAI		SFNCGGEFF	Wilson97

	nef	     135-143	  LAI		YPLTFGWCY	Culmann91,CulmannPenciolelli94	
HLA-B27					        2       C	Jardetzky91
					        R       K 
	p17	     18-27	  LAI		KIRLRPGGKK	D. Lewinsohn Per.comm.
	p17	     19-27	  LAI	        IRLRPGGKK	D. Lewinsohn Per.comm.
	p24	    263-272	  LAI		KRWIILGLNK	Nixon88,Buseyne93
	gp41	    590-597	  LAI		RYLKDQQL	Shankar96
	gp41	    791-799	  LAI     	GRRGWEALKY	Lieberman92, J. Lieberman Per.comm.
B*2703	gag	    260-269	  HIV-2		RRWIQLGLQK	S. Rowland-Jones Per.comm.
B*2705	nef	    105-114	  LAI		RRQDILDLWI	Goulder97d
	nef	     73-82	  LAI	 	QVPLRPMTYK	B. Culmann Per.comm.
	nef	    134-141	  LAI	 	RYPLTFGW	B. Culmann Per.comm.

HLA-B35						 2      C	Hill92b
						 P      Y
	p17 	    124-132	  LAI		NSSKVSQNY	RowlandJones95
	p17	     36-44	  LAI		WASRELERF	Goulder97a
	p24	    254-262	  LAI		PPIPVGDIY	RowlandJones95
	RT	    262-270	  LAI		TVLDVGDAY	B. Wilkes, D. Ruhl Per.comm.
	RT	    273-282	  III-B	 	VPLDEDFRKY	Sipsas97,Shiga96	
	RT	    328-336	  III-B		NPDIVIYQY	Sipsas97,Shiga96
	RT	    342-350	  LAI		HPDIVIYQY	RowlandJones95
	gp120	     42-52	  LAI		VPVWKEATTTL	B. Wilkes, D. Ruhl Per.comm.
	gp41	    611-619	  LAI	        TAVPWNASW	Johnson94
	nef	     74-81	  LAI		VPLRPMTY	Culmann91,CulmannPenciolelli94
	gag	    245-253	  HIV-2		NPVPVGNIY	RowlandJones95

	nef	    120-128	  LAI		YFPDWQNYT	Culmann91 and Per.comm.

	p24	    193-201	  LAI	 	GHQAAMQML	I. Kurane, K. West Per.comm.

	p17	     20-29	  LAI		RLRPGGKKKY	B. Wilkes, D. Ruhl Per.comm.
	RT	    438-446	  LAI		YPGIKVRQL	B. Wilkes, D. Ruhl Per.comm.

	p24	    306-316	  LAI		AEQASQDVKNW	Lewinsohn  Per.comm.
	gp120	     30-38	  LAI		AENLWVTVY	Borrow97	
	RT	    591-600	  LAI		GAETFYVDGA	B. Wilkes, D. Ruhl Per.comm.
	p24	    325-333	  LAI		NANPDCKTI	B. Wilkes, D. Ruhl Per.comm.
	RT	    295-302	  III-B		TAFTIPSI	Sipsas97	
	gp41	    557-565	  III-B		RAIEAQQHL	Sipsas97

	p24 	    275-282	  LAI		RMYSPTSI	B. Wilkes, D. Ruhl Per.comm.

HLA-B53						2      C	Hill92b
						P      Y
	HIV-2 gag   173-181	  HIV-2		TPYDINQML	Gotch93	

	gp120	     42-51	  LAI		VPVWKEATTT	Shankar96

	p24	    147-155	  III-B		ISPRTLNAW	Johnson91,Goulder96
	p24	    140-149	  LAI	  	TSTLQEQIGW	Goulder96	
	p24	    162-172	  LAI		KAFSPEVIPMF	Goulder96	
	p24	    240-249	  LAI		TSTLQEQIGW	Goulder96	
	p24	    311-319	  LAI		QASQEVKNW	Goulder96	
	p24	    311-319	  LAI		QASQDVKNW	Goulder96	
	nef 	    116-125	  LAI		HTQGYFPDWQ	Culmann91	
	nef 	    120-128	  LAI		YFPDWQNYT	Culmann91

	p24	    240-249	  LAI		TSTLQEQIGW	Goulder96
HLA-B60	p17	     93-101	  LAI		EIKDTKEAL	A. Trocha and S. Kalams Per.comm.

	p17	     20-29	  LAI		RLRPGGKKKY	Johnson91, B. Wilkes, D. Ruhl Per.comm.
	p24	    268-277	  LAI		LGLNKIVRMY	Johnson91
	RT	    415-426	  III-B		LVGKLNWASQIY	P. Johnson Per.comm.
	RT	    476-485	  LAI		ILKEPVHGVY	Johnson91, P. Johnson Per.comm.
	nef	     84-91	  LAI		AVDLSHFL	CulmannPenciolelli94
	nef	    117-127	  LAI		TQGYFPDWQNY	B. Culmann Per.comm.

	p24	    168-175	  LAI		VIPMFSAL	P. Goulder in press  AIDS
HLA-Cw4						 2      C	Falk94
						 Y      F
						 P      L
						 F      M
	gp120	    380-388	  LAI		SFNCGGEFF	Johnson93,Wilson97
 C*0401	p24	    308-316	  LAI		QASQEVKNW	Buseyne97	

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